changed isi distance profile to abs values

6 files changed, 9 insertions, 23 deletions

diff --git a/examples/plot.py b/examples/plot.py
index da53670..4ac8f5d 100644
--- a/examples/plot.py
+++ b/examples/plot.py
@@ -29,8 +29,6 @@ plt.figure()
 plt.plot(x, np.abs(y), '--k')
 
 print("Average: %.8f" % f.avrg())
-print("Absolute average: %.8f" % f.abs_avrg())
-
 
 f = spk.spike_distance(spike_trains[0], spike_trains[1])
 x, y = f.get_plottable_data()
diff --git a/pyspike/cython_distance.pyx b/pyspike/cython_distance.pyx
index ccf8060..178fcba 100644
--- a/pyspike/cython_distance.pyx
+++ b/pyspike/cython_distance.pyx
@@ -60,7 +60,7 @@ def isi_distance_cython(double[:] s1,
     isi_values = np.empty(N1+N2-1)
 
     with nogil: # release the interpreter to allow multithreading
-        isi_values[0] = (nu1-nu2)/fmax(nu1,nu2)
+        isi_values[0] = fabs(nu1-nu2)/fmax(nu1, nu2)
         index1 = 0
         index2 = 0
         index = 1
@@ -88,7 +88,7 @@ def isi_distance_cython(double[:] s1,
                 nu1 = s1[index1+1]-s1[index1]
                 nu2 = s2[index2+1]-s2[index2]            
             # compute the corresponding isi-distance
-            isi_values[index] = (nu1 - nu2) / fmax(nu1, nu2)
+            isi_values[index] = fabs(nu1 - nu2) / fmax(nu1, nu2)
             index += 1
         # the last event is the interval end
         spike_events[index] = s1[N1]
diff --git a/pyspike/distances.py b/pyspike/distances.py
index 3b9fe1f..08d0ed8 100644
--- a/pyspike/distances.py
+++ b/pyspike/distances.py
@@ -213,7 +213,7 @@ def isi_distance_matrix(spike_trains, indices=None):
     
     distance_matrix = np.zeros((len(indices), len(indices)))
     for i, j in pairs:
-        d = isi_distance(spike_trains[i], spike_trains[j]).abs_avrg()
+        d = isi_distance(spike_trains[i], spike_trains[j]).avrg()
         distance_matrix[i, j] = d
         distance_matrix[j, i] = d
     return distance_matrix
diff --git a/pyspike/function.py b/pyspike/function.py
index 7722cc3..bd3e2d5 100644
--- a/pyspike/function.py
+++ b/pyspike/function.py
@@ -18,7 +18,7 @@ import numpy as np
 ##############################################################
 class PieceWiseConstFunc:
     """ A class representing a piece-wise constant function. """
-    
+
     def __init__(self, x, y):
         """ Constructs the piece-wise const function.
         Args:
@@ -66,16 +66,6 @@ class PieceWiseConstFunc:
         return np.sum((self.x[1:]-self.x[:-1]) * self.y) / \
             (self.x[-1]-self.x[0])
 
-    def abs_avrg(self):
-        """ Computes the average of the abs value of the piece-wise const
-        function:
-        a = 1/T int |f(x)| dx where T is the length of the interval.
-        Returns:
-        - the average a.
-        """
-        return np.sum((self.x[1:]-self.x[:-1]) * np.abs(self.y)) / \
-            (self.x[-1]-self.x[0])
-
     def add(self, f):
         """ Adds another PieceWiseConst function to this function.
         Note: only functions defined on the same interval can be summed.
@@ -84,7 +74,7 @@ class PieceWiseConstFunc:
         """
         assert self.x[0] == f.x[0], "The functions have different intervals"
         assert self.x[-1] == f.x[-1], "The functions have different intervals"
-        
+
         # python implementation
         # from python_backend import add_piece_wise_const_python
         # self.x, self.y = add_piece_wise_const_python(self.x, self.y,
@@ -107,7 +97,7 @@ class PieceWiseConstFunc:
 ##############################################################
 class PieceWiseLinFunc:
     """ A class representing a piece-wise linear function. """
-    
+
     def __init__(self, x, y1, y2):
         """ Constructs the piece-wise linear function.
         Args:
diff --git a/test/test_distance.py b/test/test_distance.py
index b500b2c..6e50467 100644
--- a/test/test_distance.py
+++ b/test/test_distance.py
@@ -23,8 +23,8 @@ def test_isi():
 
     # pen&paper calculation of the isi distance
     expected_times = [0.0, 0.2, 0.3, 0.4, 0.45, 0.6, 0.7, 0.8, 0.9, 0.95, 1.0]
-    expected_isi = [-0.1/0.3, -0.1/0.3, 0.05/0.2, 0.05/0.2, -0.15/0.35,
-                    -0.25/0.35, -0.05/0.35, 0.2/0.3, 0.25/0.3, 0.25/0.3]
+    expected_isi = [0.1/0.3, 0.1/0.3, 0.05/0.2, 0.05/0.2, 0.15/0.35,
+                    0.25/0.35, 0.05/0.35, 0.2/0.3, 0.25/0.3, 0.25/0.3]
     
     t1 = spk.add_auxiliary_spikes(t1, 1.0)
     t2 = spk.add_auxiliary_spikes(t2, 1.0)
@@ -40,7 +40,7 @@ def test_isi():
     t2 = np.array([0.1, 0.4, 0.5, 0.6])
 
     expected_times = [0.0, 0.1, 0.2, 0.4, 0.5, 0.6, 1.0]
-    expected_isi = [0.1/0.2, -0.1/0.3, -0.1/0.3, 0.1/0.2, 0.1/0.2, -0.0/0.5]
+    expected_isi = [0.1/0.2, 0.1/0.3, 0.1/0.3, 0.1/0.2, 0.1/0.2, 0.0/0.5]
 
     t1 = spk.add_auxiliary_spikes(t1, 1.0)
     t2 = spk.add_auxiliary_spikes(t2, 1.0)
diff --git a/test/test_function.py b/test/test_function.py
index a579796..c5caa5a 100644
--- a/test/test_function.py
+++ b/test/test_function.py
@@ -28,8 +28,6 @@ def test_pwc():
     assert_array_almost_equal(yp, yp_expected, decimal=16)
 
     assert_almost_equal(f.avrg(), (1.0-0.5+0.5*1.5+1.5*0.75)/4.0, decimal=16)
-    assert_almost_equal(f.abs_avrg(), (1.0+0.5+0.5*1.5+1.5*0.75)/4.0,
-                        decimal=16)
 
 
 def test_pwc_add():